The allowed sequence formats are FASTA and PIR
Example of fasta format:
>HAHU Hemoglobin alpha chain - Human and chimpanzees
Example of pir format:
Hemoglobin alpha chain - Human and chimpanzees
Select a database of protein sequences from the list.
The alignment scoring matrix used by Scanps.
Scanps can output more than one alternative alignment for each sequence in the score list. Tick this option turn it on.
Select a sequence from a database using the sequence's Uniform Sequence Address (USA). See the EMBOSS documentation on USAs.
standard: Uses simple length-dependent gap penalty affine: Uses an affine gap penalty
For affine gap penalties, this is the penalty for opening a gap in an alignment.
The penalty for extending gaps in the alignment.
Only hits with an Expectation value less than this cutoff are output.
The maximum number of hits that is output
If this option is ticked, pairwise alignments are output only for hits with E-values above the cutoff.
Set the maximum number of pairwise alignments output.
Define the width of the pairwise alignments in the output.
This sets the E-value cutoff for including sequences in the multiple alignment profile that is built from the first and subsequent iterations of a scan. This is usually set to be much smaller than the E-value cutoff for the output list.
Number of search iterations. If this is greater than 1, scanps will build a search profile from the results of the initial scan and scan the database with this profile. This process is repeated N times where N is the number of iterations. The search may also stop if two successive iterations return the same set of sequences.
Output the frequency table calculated from the multiple alignment in each iteration.
Tick this option to include the profile tables in the output. These profile table are calculated from the multiple alignments in each iteration and used to search in the next iteration.
Tick this option to get the raw Scanps output without any HTML formatting.